recipe pydeseq2

A python implementation of DESeq2.

Homepage:

https://github.com/owkin/PyDESeq2

Documentation:

https://pydeseq2.readthedocs.io/en/latest

License:

MIT / MIT

Recipe:

/pydeseq2/meta.yaml

Links:

doi: 10.1101/2022.12.14.520412

package pydeseq2

versions:

0.4.12-0,  0.4.11-0,  0.4.10-0,  0.4.9-0,  0.4.8-0,  0.4.7-0,  0.4.6-0,  0.4.5-0,  0.4.4-0, 

0.4.12-0,  0.4.11-0,  0.4.10-0,  0.4.9-0,  0.4.8-0,  0.4.7-0,  0.4.6-0,  0.4.5-0,  0.4.4-0,  0.4.3-0,  0.4.2-0,  0.4.1-0,  0.4.0-0,  0.3.6-0,  0.3.5-0,  0.3.4-0,  0.3.3-0

depends anndata:

>=0.8.0

depends ipython:

depends jupyter:

depends matplotlib-base:

>=3.6.2

depends numpy:

>=1.23.0

depends pandas:

>=1.4.0

depends python:

>=3.9

depends scikit-learn:

>=1.1.0

depends scipy:

>=1.11.0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install pydeseq2

and update with::

   mamba update pydeseq2

To create a new environment, run:

mamba create --name myenvname pydeseq2

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/pydeseq2:<tag>

(see `pydeseq2/tags`_ for valid values for ``<tag>``)

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